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match neuronal structure from two different DNAs


fredreload

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  • 3 weeks later...

Probably, of course depending on how similar or dissimilar they are. This of course only works for neurons and not when including other types of cells such as immune cells.
For instance, experiments are done with different neuron lines to measure their interaction on a plate most likely don't use neurons from exactly the same individual, but I wouldn't know for sure.

-Dagl

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On 4/18/2019 at 4:13 PM, Dagl1 said:

Probably, of course depending on how similar or dissimilar they are. This of course only works for neurons and not when including other types of cells such as immune cells.
For instance, experiments are done with different neuron lines to measure their interaction on a plate most likely don't use neurons from exactly the same individual, but I wouldn't know for sure.

-Dagl

Yes master, right because everyone's genetic is slightly different based on height and size, but that shouldn't affect the cells being the building block of the body, maybe the pigment. Of course to prove whether you could get the exact same synapses of two neuronal cells with different genetics is still in debate. But if synapse is an attribute of the neuronal cell type, it should hold true unaffected by the genetics. I am not sure about pigments though, as it constitute different eye colors and hair

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11 minutes ago, fredreload said:

Yes master, right because everyone's genetic is slightly different based on height and size, but that shouldn't affect the cells being the building block of the body, maybe the pigment. Of course to prove whether you could get the exact same synapses of two neuronal cells with different genetics is still in debate. But if synapse is an attribute of the neuronal cell type, it should hold true unaffected by the genetics. I am not sure about pigments though, as it constitute different eye colors and hair

If people differ in things like eye colour because of genetics then, obviously, they will differ at the level of cells (or including neurons).

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On 4/21/2019 at 7:56 PM, Strange said:

If people differ in things like eye colour because of genetics then, obviously, they will differ at the level of cells (or including neurons).

Well let's compare a single neuron. The axon length is mostly the same for the two I speculate, or does it differ between male and female? Can you also get the same synaptic delays for the two neurons for male and female(i.e. the delay time traveling from neuron to neuron).

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22 minutes ago, Strange said:

The length of the axon will be determined by what it is connecting too. On average, I suppose axons in males will be larger because male bodies are larger on average.

 

I suppose you mean non-brain neurons (motor neurons for example)? I personally doubt that axons in the brain, on average, will be longer in males than in females. But I think that is also what you meant right?

2 hours ago, fredreload said:

Well let's compare a single neuron. The axon length is mostly the same for the two I speculate, or does it differ between male and female? Can you also get the same synaptic delays for the two neurons for male and female(i.e. the delay time traveling from neuron to neuron).

It may be a good idea to get some better fundamentals on both genetics and neural science. Regarding the question of synaptic delays, if we go super deep then maybe the distance from neuron to neuron can slightly alter traveling speed, or maybe some proteins require more or less time to be active, but this would be probably even unnoticeable within experiments that would be designed to look for these alterations.

Now if you are talking about things like, the time it takes for a signal to go from your brain to your feet, this is mostly dependent on the amount of myeline around axons.
 

If you are interested in more depth information, "The fundamentals of Neural Science, by Kandel" is an amazing book to learn about how neurons work.

-Dagl

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2 hours ago, Dagl1 said:

I suppose you mean non-brain neurons (motor neurons for example)? I personally doubt that axons in the brain, on average, will be longer in males than in females. But I think that is also what you meant right?

It may be a good idea to get some better fundamentals on both genetics and neural science. Regarding the question of synaptic delays, if we go super deep then maybe the distance from neuron to neuron can slightly alter traveling speed, or maybe some proteins require more or less time to be active, but this would be probably even unnoticeable within experiments that would be designed to look for these alterations.

Now if you are talking about things like, the time it takes for a signal to go from your brain to your feet, this is mostly dependent on the amount of myeline around axons.
 

If you are interested in more depth information, "The fundamentals of Neural Science, by Kandel" is an amazing book to learn about how neurons work.

-Dagl

Hi sir, the only reason I look into the genetics of the brain is because I am curious about swapping consciousness. This might be a bit jumping the gun as it is way ahead of the topic, but I find that you sir, might have the knowledge to interpret such a thing.

To begin with, our consciousness stays with us throughout our life. And as we fall asleep, the nerve electrical signals retract to the brain stem in a hibernation state. Therefore, I conclude that the consciousness region of the brain must exist inside the brain stem, based on a scientific paper, which sort of rules out the entire cerebellum.

Now, to go one step further, let's take a look at the brain stem. A brain stem consists of multiple nucleus form from groups of neurons. The nucleus, from my speculation, resembles that of a ping pong ball. And it is from the repeating rhythm of the nerve signals running within this ping pong ball that generates a soul, a consciousness. Watch the video below to get a sense of rhythm based on the brain wave.

Now we all know that a nerve signal running in the neurons generates an electric field like a capacitor because of the opposite polarity of sodium and potassium inside and outside the neuron. This means this ping pong ball of consciousness has an electric field emanating out in all directions like a light bulb.

Now, what distinguishes a consciousness from another and makes it unique? If you look at the ping pong balls, they all look the same, but clearly they are of different consciousnesses, therefore I must rule out the possibility that the shape of the nucleus(group of neurons) of ping pong ball is the key to the uniqueness of consciousnesses. This means someone could have a cylinder nucleus head or pyramid nucleus head, no I ruled all that out. (But I have to note that the shape of the brain might have an implication on the generation of the resonance of consciousness, the shape of the brain might not constitute the uniqueness of the consciousness, but it does matter on constructing a consciousness).

Then what is the difference between the two ping pong balls of consciousnesses. Based on the property left of a neuron, it must be the axon length and the synaptic delays. Since you have just ruled out the idea of axon length, based on the nerve signal traveling speed of 150m/s the distance of axons should be of marginal differences to consider.

That leaves the rhythm, the synaptic delays as the key to the uniqueness of consciousnesses. Now could two neurons coming from two different genetics generate the same synaptic delays. This would be the key to mind uploading as you match the rhythm from one brain to the next. Clearly if it is of an identical clone or twin of same genetics I could match the synaptic delays with ease. But if you cross reference it to a different individual, could the same synaptic delays be built on the neurons thereby matching the rhythm of two ping pong balls and consciousnesses?

 

 

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35 minutes ago, fredreload said:

Hi sir, the only reason I look into the genetics of the brain is because I am curious about swapping consciousness. This might be a bit jumping the gun as it is way ahead of the topic, but I find that you sir, might have the knowledge to interpret such a thing.

To begin with, our consciousness stays with us throughout our life. And as we fall asleep, the nerve electrical signals retract to the brain stem in a hibernation state. Therefore, I conclude that the consciousness region of the brain must exist inside the brain stem, based on a scientific paper, which sort of rules out the entire cerebellum.

Now, to go one step further, let's take a look at the brain stem. A brain stem consists of multiple nucleus form from groups of neurons. The nucleus, from my speculation, resembles that of a ping pong ball. And it is from the repeating rhythm of the nerve signals running within this ping pong ball that generates a soul, a consciousness. Watch the video below to get a sense of rhythm based on the brain wave.

Now we all know that a nerve signal running in the neurons generates an electric field like a capacitor because of the opposite polarity of sodium and potassium inside and outside the neuron. This means this ping pong ball of consciousness has an electric field emanating out in all directions like a light bulb.

Now, what distinguishes a consciousness from another and makes it unique? If you look at the ping pong balls, they all look the same, but clearly they are of different consciousnesses, therefore I must rule out the possibility that the shape of the nucleus(group of neurons) of ping pong ball is the key to the uniqueness of consciousnesses. This means someone could have a cylinder nucleus head or pyramid nucleus head, no I ruled all that out. (But I have to note that the shape of the brain might have an implication on the generation of the resonance of consciousness, the shape of the brain might not constitute the uniqueness of the consciousness, but it does matter on constructing a consciousness).

Then what is the difference between the two ping pong balls of consciousnesses. Based on the property left of a neuron, it must be the axon length and the synaptic delays. Since you have just ruled out the idea of axon length, based on the nerve signal traveling speed of 150m/s the distance of axons should be of marginal differences to consider.

That leaves the rhythm, the synaptic delays as the key to the uniqueness of consciousnesses. Now could two neurons coming from two different genetics generate the same synaptic delays. This would be the key to mind uploading as you match the rhythm from one brain to the next. Clearly if it is of an identical clone or twin of same genetics I could match the synaptic delays with ease. But if you cross reference it to a different individual, could the same synaptic delays be built on the neurons thereby matching the rhythm of two ping pong balls and consciousnesses?

 

 

Hmm I think you make some assumptions/jumps that I wouldn't (doesn't mean they are wrong, although I personally wouldn't be so sure); Just because we keep our consciousness after sleeping, doesn't have to mean that it is located within the brain stem. What if it it is more like a computer which gets rebooted, or in our case, the neurons in the cortex go into "cleaning mode" (look into the glymphatic system if you are interested)?

I honestly think that you would do very good by FIRST learning the more indepth details, then using your quite speculative mind on the more... current questions? As a scientist I feel like you make too many conclusions, but you seem very interested in this stuff, which is why I would recommend you to first learn the foundations, then speculate. Most people in science are quite... rigid (mostly due to how science works), but currently for you there are too many unknowns.

If you want, I can help you through several layers of (neuro)science, but it does require you to read a lot and not assume but just read for a bit, if you are interested, please send me a PM.
 

-Dagl

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3 hours ago, Dagl1 said:

Hmm I think you make some assumptions/jumps that I wouldn't (doesn't mean they are wrong, although I personally wouldn't be so sure); Just because we keep our consciousness after sleeping, doesn't have to mean that it is located within the brain stem. What if it it is more like a computer which gets rebooted, or in our case, the neurons in the cortex go into "cleaning mode" (look into the glymphatic system if you are interested)?

I honestly think that you would do very good by FIRST learning the more indepth details, then using your quite speculative mind on the more... current questions? As a scientist I feel like you make too many conclusions, but you seem very interested in this stuff, which is why I would recommend you to first learn the foundations, then speculate. Most people in science are quite... rigid (mostly due to how science works), but currently for you there are too many unknowns.

If you want, I can help you through several layers of (neuro)science, but it does require you to read a lot and not assume but just read for a bit, if you are interested, please send me a PM.
 

-Dagl

It is alright, thank you for taking the time to read my response. I understand the rigidity of science and thank you for your patience :D .

Sincerely,

fredreload

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  • 2 weeks later...
On 4/24/2019 at 5:09 PM, Strange said:

Absolutely. 

There are so many factors that can affect brain development, I wouldn’t dare comment!

I'm thinking of two pathways. One that increase the number of dendrites on a neuron, and another decrease the dendrites on the neuron. I mean you don't just stick a gum onto a neuron to form a new dendrite. The neuron comes with a fixed number of dendrites and it is up to the gene expression to change the number of dendrites it branch out from the neuron. Now when dendrites touch each other, it form synapses. I am not sure if my speculation is correct but do verify this for me Strange. Thanks in advance.

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9 minutes ago, fredreload said:

I'm thinking of two pathways. One that increase the number of dendrites on a neuron, and another decrease the dendrites on the neuron. I mean you don't just stick a gum onto a neuron to form a new dendrite. The neuron comes with a fixed number of dendrites and it is up to the gene expression to change the number of dendrites it branch out from the neuron. Now when dendrites touch each other, it form synapses. I am not sure if my speculation is correct but do verify this for me Strange. Thanks in advance.

The growth of dendrites (number, length, branching) is not determined by genes. It is a dynamic process that is changed by interactions with other neurons, environment, neuronal activity, disease and many other factors.

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15 minutes ago, Strange said:

The growth of dendrites (number, length, branching) is not determined by genes. It is a dynamic process that is changed by interactions with other neurons, environment, neuronal activity, disease and many other factors.

Hmm, I think the dynamic process is correct about dendritic growth, but when the embryo first form, does the dendrite randomly branch out in all directions from a neuron? Why does it branch out 5 dendrites instead of 4 dendrites, what is governing this?

This is an image example https://sapienlabs.co/dendrite-complexity-and-intelligence/

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12 hours ago, CharonY said:

The connections are formed via stimulating signaling affecting dendritic (and axonal) growth. As Strange indicated, their expression is dynamic.

Good call, the neuron does generates its own electrical signal due to ion imbalance when it is just born and is not connected to other neurons. I speculate.

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1 hour ago, fredreload said:

Good call, the neuron does generates its own electrical signal due to ion imbalance when it is just born and is not connected to other neurons. I speculate.

What would this signal do, where does it lead to and... what type of neuron are you talking about?

@Strange@CharonY
While the growth is partly based on signalling and is dynamic, genes of course do play a role, and differences in genes/proteins that are involved in neuronal growth (axonal and dendritic) will possibly result in an increase or decrease of the number/length/branching pattern(?), don't you agree? 

 

Also fredreload, why not just read up on neuronal development? Instead of coming up with speculations that you then want to have verified, isn't it a lot easier to just read up on this stuff?

-Dagl

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15 minutes ago, Dagl1 said:

While the growth is partly based on signalling and is dynamic, genes of course do play a role, and differences in genes/proteins that are involved in neuronal growth (axonal and dendritic) will possibly result in an increase or decrease of the number/length/branching pattern(?), don't you agree? 

Of course. I just meant that the growth is not directly determined (predetermined?) by the genes. 

But of course the whole process is defined by the genes, and the growth and pruning of dendrites is controlled by gene expression (which is, in turn, controlled by the factors mentioned).

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Just now, Strange said:

Of course. I just meant that the growth is not directly determined (predetermined?) by the genes. 

But of course the whole process is defined by the genes, and the growth and pruning of dendrites is controlled by gene expression (which is, in turn, controlled by the factors mentioned).

Sorry for the nitpicking, I just feel that for Fredreload it may be important to be as clear as possible;p I'm pretty sure you know what you are talking about, but I could already see how things are going to fuel more speculation.

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2 hours ago, Dagl1 said:

Sorry for the nitpicking, I just feel that for Fredreload it may be important to be as clear as possible;p I'm pretty sure you know what you are talking about, but I could already see how things are going to fuel more speculation.

Well, I try to find the best solution on Google, but there are all kinds of saying and research including epigenetics, and the research on ncbl which is technical yet complex at the time. It is a bit hard for me to just find a research on such as if epigenetics determine the number of dendrites presented on a neuron. The closest I found is RNA modification in the brain on Sea Snails. Which in terms should modify the dendrites because the sea snail's behavior changes, but they did not go over dendritic changes at all. I did find and is pretty sure on the synapse formation from Glutamate or GABA signaling. So the only thing I am unsure on is the dendritic growth which has been clarified thanks to you else I would probably have to go over the sea snail article again( I can't believe they did not analyze the dendritic patterns afterward). And as a record it does seem like the neuron's DNA holds a record of the dendrites because the dendrites, once cut, could easily be regenerated.

Edited by fredreload
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Why do the dendrites HAVE to be modified if a sea snails behavior changes?
Can you link this particular article?
Why does DNA HAVE to hold a record of the dendrites, when they can regenerate; there are other possibilities that aren't the DNA right?

Regarding reading up on it, I think it is a lot more helpful for you to first find some reviews of axonal and neuronal growth, the cell signalling components and intracellular pathways involved. I think general information is a lot more helpful for you than very in depth (experimental) articles. 

The following paste is from my own notes, they the first ones date back 3 or 4 years, when I personally got very interested in the molecular mechanisms of memory, they may be interesting for you (although definitely not all of them, as not all are about neuroscience, either way this may be helpful!).
 

This is an interesting article which shows the basis of LTP quite well.

(Kandel, 2012) The molecular biology of memory: cAMP, PKA, CRE, CREB-1, CREB-2, and CPEB http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514210/


This shows the differences of LTP in different neurons, quite interesting but specific.

 

A quite specific article but made by our own university!
(Prickaerts et al, 2014) Improved Long-Term Memory via Enhancing cGMP-PKG Signaling Requires cAMP-PKA Signaling

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4207334/

An introduction into metabrotropic gutamate receptors.

(Gerber et al, 2007) Metabotropic glutamate receptors: intracellular signaling pathways
http://www.sciencedirect.com/science/article/pii/S1471489206001706

 

An introduction into NMDAR and AMPA involvement in LTP/LTD
(Lüscher et al, 2012) NMDA Receptor-Dependent Long-Term Potentiation and Long-Term Depression (LTP/LTD)
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367554/

The rules of spine learning, 15 rules on how spines change.
(Kasai et al, 2010) Learning rules and persistence of dendritic spines
http://onlinelibrary.wiley.com/doi/10.1111/j.1460-9568.2010.07344.x/full

A very good introduction into histone post translational modifications
(Bannister et al, 2011) Regulation of chromatin by histone modifications
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3193420/

An indepth article surrounding transcription and the 3D genome
(Rajarajan et al, 2016) Spatial genome organization and cognition
http://www.nature.com/nrn/journal/v17/n11/pdf/nrn.2016.124.pdf

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5 hours ago, Dagl1 said:

Why do the dendrites HAVE to be modified if a sea snails behavior changes?
Can you link this particular article?
Why does DNA HAVE to hold a record of the dendrites, when they can regenerate; there are other possibilities that aren't the DNA right?

Sir,

Hi, I will answer the above questions.

1. The dendrites should be modified because they inject RNA into the sea snail's brain(RNA->change gene expression in cell), which is likely to modify the gene expression and epigenetics of the neurons. They however, went on to speculate that the nucleus is doing the work in which they did not examine the changes in dendritic wiring. The proof I want is that RNA modifies dendritic wirings because of epigenetics, that way you can change the number/length of dendrites through different pathways. The article is posted below.

https://www.sciencealert.com/memory-transferred-between-sea-snails-rna-engram

2. Well this article I found suggested that the dendrites grew back after they cut it off in drosphila neurons(sorry I can only find drosphila example). The article says that there is a different regeneration pathway for axon and dendrites, but this is not the point I want to prove. The dendrites regenerate suggesting that the epigenetics keep a backup of the structure of the dendrite's length and numbers. Of course the dendrite could have as well grew back anew from the neuron, but they used the term regenerate, and I am unsure on the time frame it took for growth vs regeneration as well. I read a few years ago that the epigenetics supposed to hold a record of the length and numbers of the dendrites, but I've long since lost that paper. Epigenetics is more of a new field for me, I interpret it as a different way of gene expression. Below is the article for dendrite regeneration.

https://www.sciencedirect.com/science/article/pii/S2211124713007675

P.S. My eventual goal is to use optogenetics/pathways to remap the entire brain, dendrites and synapses.

Edited by fredreload
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4 hours ago, fredreload said:

Sir,

Hi, I will answer the above questions.

1. The dendrites should be modified because they inject RNA into the sea snail's brain(RNA->change gene expression in cell), which is likely to modify the gene expression and epigenetics of the neurons. They however, went on to speculate that the nucleus is doing the work in which they did not examine the changes in dendritic wiring. The proof I want is that RNA modifies dendritic wirings because of epigenetics, that way you can change the number/length of dendrites through different pathways. The article is posted below.

https://www.sciencealert.com/memory-transferred-between-sea-snails-rna-engram

2. Well this article I found suggested that the dendrites grew back after they cut it off in drosphila neurons(sorry I can only find drosphila example). The article says that there is a different regeneration pathway for axon and dendrites, but this is not the point I want to prove. The dendrites regenerate suggesting that the epigenetics keep a backup of the structure of the dendrite's length and numbers. Of course the dendrite could have as well grew back anew from the neuron, but they used the term regenerate, and I am unsure on the time frame it took for growth vs regeneration as well. I read a few years ago that the epigenetics supposed to hold a record of the length and numbers of the dendrites, but I've long since lost that paper. Epigenetics is more of a new field for me, I interpret it as a different way of gene expression. Below is the article for dendrite regeneration.

https://www.sciencedirect.com/science/article/pii/S2211124713007675

P.S. My eventual goal is to use optogenetics/pathways to remap the entire brain, dendrites and synapses.

Ahh I see now; that article refers to a study in which they took RNA from a trained sea snail and put that in a naive sea snail, which then showed a similar behavior. My question, though, is: why do you think that it is the dendrites and not other parts that are modified by this addition of RNA. There are more parts to neuronal signal transmission than just the synapse.

The other question was meant in a similar manner: why does it HAVE to be DNA (note; epigenetics is not confined to just DNA) or even epigenetics. Can't it be that the proteins or their mRNA are already in place (and primed) to (re)build those dendritic spines after they are cut. 

The reason for me asking these questions in this manner is because in both cases there are other options which are ignored. If you can think of a different mechanism then you cannot conclude that it HAS to be 1 mechanism.

Regarding epigenetics, other examples are: histone modifications and mRNA modifications.

Kind regards,
Dagl

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4 minutes ago, Dagl1 said:

Ahh I see now; that article refers to a study in which they took RNA from a trained sea snail and put that in a naive sea snail, which then showed a similar behavior. My question, though, is: why do you think that it is the dendrites and not other parts that are modified by this addition of RNA. There are more parts to neuronal signal transmission than just the synapse.

The other question was meant in a similar manner: why does it HAVE to be DNA (note; epigenetics is not confined to just DNA) or even epigenetics. Can't it be that the proteins or their mRNA are already in place (and primed) to (re)build those dendritic spines after they are cut. 

The reason for me asking these questions in this manner is because in both cases there are other options which are ignored. If you can think of a different mechanism then you cannot conclude that it HAS to be 1 mechanism.

Regarding epigenetics, other examples are: histone modifications and mRNA modifications.

Kind regards,
Dagl

Sir,

1. Well in this regard we sort of have to understand consciousness and that which affect memory as a whole. Consciousness as I see it is an electrical resonance that occurs within the brain. To skip over all the complex theory I ask what could possibly affect a memory in a brain. The answer would be "dendrite numbers, dendrite length, and synaptic delays". I don't think axon length has any affect on memory, it could.

So the snail's memory is changed by the RNA, and since the memory is changed it must affect "dendrite numbers, dendrite length, or synaptic delays". Synapses is built dynamically as I see it from glutamate or GABA receptors, therefore it must not be affected by RNA. What is left would be "dendrite number and dendrite length" that could be changed in this case.

2. Well the dendritic build is either dynamic or affected by DNA. If I have to remap the dendrite on a neuron I will either have to "cut the dendrite" or "change the RNA/gene expression". I just want to be precise in this regard.

Sincerely,

Fred

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15 hours ago, fredreload said:

Sir,

1. Well in this regard we sort of have to understand consciousness and that which affect memory as a whole. Consciousness as I see it is an electrical resonance that occurs within the brain. To skip over all the complex theory I ask what could possibly affect a memory in a brain. The answer would be "dendrite numbers, dendrite length, and synaptic delays". I don't think axon length has any affect on memory, it could.

So the snail's memory is changed by the RNA, and since the memory is changed it must affect "dendrite numbers, dendrite length, or synaptic delays". Synapses is built dynamically as I see it from glutamate or GABA receptors, therefore it must not be affected by RNA. What is left would be "dendrite number and dendrite length" that could be changed in this case.

2. Well the dendritic build is either dynamic or affected by DNA. If I have to remap the dendrite on a neuron I will either have to "cut the dendrite" or "change the RNA/gene expression". I just want to be precise in this regard.

Sincerely,

Fred

Firstly, there are more things than just dendrite number, length and synaptic delays which are part of memory formation (see LTP/LTD).
You need to go and look into the basics before you make conclusions; the idea that "because synapses are build dynamically it must not be affected by RNA" is wrong. Synapses can and are definitely affected by and partly the result of RNA.

I don't understand what you mean by point 2. 
Again, I think you need to make no conclusions, don't speculate and instead start with studying how most of this stuff works. Read the articles I mentioned, read a lot more and then maybe it is time to speculate.

-Dagl

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